Dr Vlad Teif

Gautam, P., Ciuta, I., Teif, VB. and Sinha, SK., (2024). Predicting p53-dependent cell transitions from thermodynamic models. The Journal of Chemical Physics. 161 (13), 135101-

Piroeva, KV., McDonald, C., Xanthopoulos, C., Fox, C., Clarkson, CT., Mallm, J-P., Vainshtein, Y., Ruje, L., Klett, LC., Stilgenbauer, S., Mertens, D., Kostareli, E., Rippe, K. and Teif, VB., (2023). Nucleosome repositioning in chronic lymphocytic leukemia. Genome Research. 33 (10), 1649-1661

Shtumpf, M., Piroeva, KV., Agrawal, SP., Jacob, DR. and Teif, VB., (2022). NucPosDB: a database of nucleosome positioning in vivo and nucleosomics of cell-free DNA. Chromosoma. 131 (1-2), 19-28

Thorn, GJ., Clarkson, CT., Rademacher, A., Mamayusupova, H., Schotta, G., Rippe, K. and Teif, VB., (2022). DNA sequence-dependent formation of heterochromatin nanodomains.. Nature Communications. 13 (1), 1861-

Belokopytova, P., Viesná, E., Chiliński, M., Qi, Y., Salari, H., Di Stefano, M., Esposito, A., Conte, M., Chiariello, AM., Teif, VB., Plewczynski, D., Zhang, B., Jost, D. and Fishman, V., (2022). 3DGenBench: a web-server to benchmark computational models for 3D Genomics. Nucleic Acids Research. 50 (W1), W4-W12

Cucinotta, CE., Martin, BJE., Noé González, M., Raman, P., Teif, VB. and Vlaming, H., (2021). Strength is in engagement The rise of an online scientific community during the COVID‐19 pandemic. EMBO Reports. 22 (5), e52612-

Hedley, JG., Teif, VB. and Kornyshev, AA., (2021). Nucleosome-induced homology recognition in chromatin. Journal of The Royal Society Interface. 18 (179), 20210147-20210147

Mohr, A., Chu, T., Clarkson, C., Brooke, G., Teif, V. and Zwacka, R., (2021). Fas-threshold Signalling in MSCs Promotes Pancreatic Cancer Progression and Metastasis. Cancer Letters. 519, 63-77

Antwi, EB., Olins, A., Teif, VB., Bieg, M., Bauer, T., Gu, Z., Brors, B., Eils, R., Olins, D. and Ishaque, N., (2020). Whole-genome fingerprint of the DNA methylome during chemically induced differentiation of the human AML cell line HL-60/S4. Biology Open. 9 (2), bio044222-

Teif, V., (2020). Soft power of non-consensus protein-DNA binding. Biophysical Journal. 118 (8), 1797-1798

Teif, V., Gould, T., Clarkson, C., Boyd, L., Antwi, E., Ishaque, N., Olins, A. and Olins, D., (2020). Linker histone epitopes are hidden by in situ higher-order chromatin structure. Epigenetics and Chromatin. 13 (1), 26-

Antwi, EB., Olins, A., Teif, VB., Bieg, M., Bauer, T., Gu, Z., Brors, B., Eils, R., Olins, D. and Ishaque, N., (2020). Whole-genome fingerprint of the DNA methylome during chemically induced differentiation of the human AML cell line HL-60/S4.. Biology open

Wiehle, L., Thorn, G., Raddatz, G., Clarkson, C., Rippe, K., Lyko, F., Breiling, A. and Teif, V., (2019). DNA (de)methylation in embryonic stem cells controls CTCF-dependent chromatin boundaries. Genome Research. 29 (5), 750-761

Mallm, JP., Iskar, M., Ishaque, N., Klett, LC., Kugler, SJ., Muino, JM., Teif, VB., Poos, AM., Großmann, S., Erdel, F., Tavernari, D., Koser, SD., Schumacher, S., Brors, B., König, R., Remondini, D., Vingron, M., Stilgenbauer, S., Lichter, P., Zapatka, M., Mertens, D. and Rippe, K., (2019). Linking aberrant chromatin features in chronic lymphocytic leukemia to transcription factor networks. Molecular Systems Biology. 15 (5), e8339-

Clarkson, CT., Deeks, EA., Samarista, R., Mamayusupova, H., Zhurkin, VB. and Teif, VB., (2019). CTCF-dependent chromatin boundaries formed by asymmetric nucleosome arrays with decreased linker length. Nucleic Acids Research. 47 (21), 11181-11196

Pavlaki, I., Docquier, F., Chernukhin, I., Kita, G., Gretton, S., Clarkson, CT., Teif, VB. and Klenova, E., (2018). Poly(ADP-ribosyl)ation associated changes in CTCF-chromatin binding and gene expression in breast cells. Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms. 1861 (8), 781-730

Vainshtein, Y., Rippe, K. and Teif, VB., (2017). NucTools: analysis of chromatin feature occupancy profiles from high-throughput sequencing data. BMC Genomics. 18 (1), 158-

Teif, VB., Mallm, J-P., Sharma, T., Mark Welch, DB., Rippe, K., Eils, R., Langowski, J., Olins, AL. and Olins, DE., (2017). Nucleosome repositioning during differentiation of a human myeloid leukemia cell line. Nucleus. 8 (2), 188-204

Teif, VB., (2016). Nucleosome positioning: resources and tools online. Briefings in Bioinformatics. 17 (5), 745-757

B. Teif, V. and G. Cherstvy, A., (2016). Chromatin and epigenetics: current biophysical views. AIMS Biophysics. 3 (1), 88-98

Salih, BF., Teif, VB., Tripathi, V. and Trifonov, EN., (2015). Strong nucleosomes of mouse genome including recovered centromeric sequences. Journal of Biomolecular Structure and Dynamics. 33 (6), 1164-1175

Teif, VB., Kepper, N., Yserentant, K., Wedemann, G. and Rippe, K., (2015). Affinity, stoichiometry and cooperativity of heterochromatin protein 1 (HP1) binding to nucleosomal arrays. Journal of Physics: Condensed Matter. 27 (6), 064110-064110

Cherstvy, AG. and Teif, VB., (2014). Electrostatic effect of H1-histone protein binding on nucleosome repeat length. Physical Biology. 11 (4), 044001-044001

Beshnova, DA., Cherstvy, AG., Vainshtein, Y. and Teif, VB., (2014). Regulation of the nucleosome repeat length in vivo by the DNA sequence, protein concentrations and long-range interactions.. PLoS Computational Biology. 10 (7), e1003698-e1003698

Teif, VB., Beshnova, DA., Vainshtein, Y., Marth, C., Mallm, J-P., Höfer, T. and Rippe, K., (2014). Nucleosome repositioning links DNA (de)methylation and differential CTCF binding during stem cell development. Genome Research. 24 (8), 1285-1295

Diermeier, S., Kolovos, P., Heizinger, L., Schwartz, U., Georgomanolis, T., Zirkel, A., Wedemann, G., Grosveld, F., Knoch, TA., Merkl, R., Cook, PR., Längst, G. and Papantonis, A., (2014). TNFα signalling primes chromatin for NF-κB binding and induces rapid and widespread nucleosome repositioning. Genome Biology. 15 (12), 536-

Schöpflin, R., Teif, VB., Müller, O., Weinberg, C., Rippe, K. and Wedemann, G., (2013). Modeling nucleosome position distributions from experimental nucleosome positioning maps. Bioinformatics. 29 (19), 2380-2386

Teif, VB., Erdel, F., Beshnova, DA., Vainshtein, Y., Mallm, JP. and Rippe, K., (2013). Taking into account nucleosomes for predicting gene expression. Methods. 62 (1), 26-38

Cherstvy, AG. and Teif, VB., (2013). Structure-driven homology pairing of chromatin fibers: the role of electrostatics and protein-induced bridging. Journal of Biological Physics. 39 (3), 363-385

Teif, VB., Vainshtein, Y., Caudron-Herger, M., Mallm, J-P., Marth, C., Höfer, T. and Rippe, K., (2012). Genome-wide nucleosome positioning during embryonic stem cell development. Nature Structural & Molecular Biology. 19 (11), 1185-1192

Teǐf, VB., Shkrobkov, AV., Egorova, VP. and Krot, VI., (2012). [Nucleosomes in gene regulation: theoretical approaches].. Molekuliarnaia biologiia. 46 (1), 3-13

Teif, VB. and Rippe, K., (2012). Calculating transcription factor binding maps for chromatin. Briefings in Bioinformatics. 13 (2), 187-201

Teif, VB., Shkrabkou, AV., Egorova, VP. and Krot, VI., (2012). Nucleosomes in gene regulation: Theoretical approaches. Molecular Biology. 46 (1), 1-10

Teif, VB. and Bohinc, K., (2011). Condensed DNA: Condensing the concepts. Progress in Biophysics and Molecular Biology. 105 (3), 208-222

Teif, VB. and Rippe, K., (2011). Nucleosome mediated crosstalk between transcription factors at eukaryotic enhancers. Physical Biology. 8 (4), 044001-044001

Teif, VB. and Rippe, K., (2010). Statistical-mechanical lattice models for protein-DNA binding in chromatin. Journal of Physics: Condensed Matter. 22 (41), 414105-414105

Teif, VB., (2010). Predicting Gene-Regulation Functions: Lessons from Temperate Bacteriophages. Biophysical Journal. 98 (7), 1247-1256

Teif, VB., Ettig, R. and Rippe, K., (2010). A Lattice Model for Transcription Factor Access to Nucleosomal DNA. Biophysical Journal. 99 (8), 2597-2607

Teif, VB. and Rippe, K., (2009). Predicting nucleosome positions on the DNA: combining intrinsic sequence preferences and remodeler activities. Nucleic Acids Research. 37 (17), 5641-5655

Teif, VB., Harries, D., Lando, DY. and Ben‐Shaul, A., (2008). Matrix formalism for site‐specific binding of unstructured proteins to multicomponent lipid membranes. Journal of Peptide Science. 14 (4), 368-373

Teif, VB., Harries, D., Lando, DY. and Ben-Shaul, A., (2008). Matrix formalism for site-specific binding of unstructured proteins to multicomponent lipid membranes. JOURNAL OF PEPTIDE SCIENCE. 14 (4), 368-373

Teif, VB., (2007). General transfer matrix formalism to calculate DNA–protein–drug binding in gene regulation: application to O R operator of phage λ. Nucleic Acids Research. 35 (11), e80-e80

Teif, VB., (2005). Ligand-Induced DNA Condensation: Choosing the Model. Biophysical Journal. 89 (4), 2574-2587

Teif, VB., Haroutiunian, SG., Vorob'ev, VI., Lando, DY. and Ivanov, V., (2002). Short-Range Interactions and Size of Ligands Bound to DNA Strongly Influence Adsorptive Phase Transition Caused by Long-Range Interactions. Journal of Biomolecular Structure and Dynamics. 19 (6), 1093-1100

Lando, DY. and Teif, VB., (2002). Modeling of DNA Condensation and Decondensation Caused by Ligand Binding. Journal of Biomolecular Structure and Dynamics. 20 (2), 215-222

Teif, VB. and Yu Lando, D., (2001). Calculations of DNA condensation caused by ligand adsorption. Molekulyarnaya Biologiya. 35 (1), 117-119

Teif, VB. and Lando, DY., (2001). Calculations of DNA condensation caused by ligand adsorption. Molecular Biology. 35 (1), 106-107

Lando, DY. and Teif, VB., (2000). Long-Range Interactions between Ligands Bound to a DNA Molecule Give Rise to Adsorption with the Character of Phase Transition of the First Kind. Journal of Biomolecular Structure and Dynamics. 17 (5), 903-911

Schöpflin, R., Müller, O., Weinberg, C., Teif, VB., Rippe, K. and Wedemann, G., (2014). Modeling Effects of Nucleosome Positioning in Short and Long Chromatin Fibers

Teif, V., Beshnova, DA., Vainshtein, Y., Marth, C., Mallm, J-P., Hoefer, T. and Rippe, K., (2014). Nucleosome rearrangement as a feedback mechanism between DNA methylation and transcription factor binding

Schöpflin, R., Teif, VB., Müller, O., Weinberg, C., Rippe, K. and Wedemann, G., (2013). Modeling Long Chromatin Fibers based on In-Vivo Nucleosome Positioning Maps

Beshnova, DA., Rippe, K. and Teif, VB., (2013). A novel method to calculate transcription factor binding in chromatin

Andrianov, AM. and Teif, VB., (2007). 3D structure model for a peptide presenting the immunogenic crown of the HIV-1 GP120 V3 loop

Teif, VB., (2007). General transfer matrix formalism to calculate DNA-protein binding in gene regulation: Applications to the lambda-switch and beyond

Lando, DY., Fridman, AS. and Teif, VB., (2007). Calculation of DNA-ligand binding characterized by the infinite radius of interactions of adsorbed ligands

Teif, V., (2005). Ligand-induced DNA condensation: Theory and experiments

Teif, VB., Vorob'ev, VI. and Lando, DY., (2002). A single DNA chemical modification by cisplatin may cause long-range changes in protein binding to DNA. Results of computer modeling.

Clarkson, CT., Deeks, EA., Samarista, R., Mamayusupova, H., Zhurkin, VB. and Teif, VB., (2019). CTCF-dependent chromatin boundaries formed by asymmetric nucleosome arrays with decreased linker length

Antwi, EB., Olins, A., Teif, VB., Bieg, M., Bauer, T., Gu, Z., Brors, B., Eils, R., Olins, D. and Ishaque, N., (2019). Whole-genome fingerprint of the DNA methylome during chemically induced differentiation of the human AML cell line HL-60/S4

Pavlaki, I., Docquier, F., Chernukhin, I., Kita, G., Gretton, S., Teif, V. and Klenova, E., (2018). Poly(ADP-ribosyl)ation associated changes in CTCF-chromatin binding and gene expression in breast cells

Teif, VB., (2013). Science 3.0: Corrections to the Science 2.0 paradigm